+ Multiple sequence alignment services are accessed from the Alignment + submenu of the Alignment Window's Web Service menu. + When an entry from one of these menus is selected, either the + currently selected residues, or the whole sequence set (if there is + no selection or only one sequence is selected) will be submitted for + multiple sequence alignment. +
+There are two kinds of multiple sequence alignment operations + available: +
-
+
- alignment - where a new alignment is constructed + from the input +
- realignment - where any aligned sequences will be + used by the service to construct a profile based alignment of the + remaining unaligned sequences +
Most alignment services are provided by the + JABAWS framework, which allows you to + customise the precise parameters used when running each alignment + program. In addition to the 'Default settings', you may choose from a + range of alignment preset settings, or create your own using the + 'Edit Settings And Run ..' dialog + box. + +
+ Alignment programs supported by JABAWS.
Versions
+ shown are those bundled with JABAWS 2.01 - if you are using a
+ different server, check its home page to find out which versions are
+ provided.
+
-
+
- Clustal Omega and + Clustal W (version 2.0.12) +
- Mafft + (version 6.8.57b) +
- Muscle (version + 3.8.31) +
- Tcoffee + (version 8.99) +
- Probcons + (version 1.12)
Multiple Alignments of Sequences with hidden
-columns
-Multiple alignment services are 'column separable' analysis operations.
-If the input contains hidden
-columns then each visible segment of the input sequence set will be
-submitted for alignment separately, and the results concatenated (with
-the hidden regions preserved) once all alignment functions have
-completed. Each sub-job's state is reported in its own tab:
-
-
+ Multiple Alignments of Sequences with hidden
+ columns
Multiple alignment services are 'column
+ separable' analysis operations. If the input contains hidden columns then
+ each visible segment of the input sequence set will be submitted for
+ alignment separately, and the results concatenated (with the hidden
+ regions preserved) once all alignment functions have completed. Each
+ sub-job's state is reported in its own tab:
+
+
+